Small proteins, encoded by small open reading frames, are only beginning to emerge with the current advancement of omics technology and bioinformatics. There is increasing evidence that small proteins play roles in diverse critical biological functions, such as adjusting cellular metabolism, regulating other protein activities, controlling cell cycles, and affecting disease physiology. In prokaryotes such as bacteria, the small proteins are largely unexplored for their sequence space and functional groups. For most bacterial species from a natural community, the sample cannot be easily isolated or cultured, and the bacterial peptides must be better characterized in a metagenomic manner. The bacterial peptides identified from metagenomic samples can not only enrich the pool of small proteins but can also reveal the community-specific microbe ecology information from a small protein perspective. In this study, metaBP (Bacterial Peptides for metagenomic sample) has been developed as a comprehensive toolkit to explore the small protein universe from metagenomic samples. It takes raw sequencing reads as input, performs protein-level meta-assembly, and computes bacterial peptide homolog groups with sample-specific mutations. The metaBP also integrates general protein annotation tools as well as our small protein-specific machine learning module metaBP-ML to construct a full landscape for bacterial peptides. The metaBP-ML shows advantages for discovering functions of bacterial peptides in a microbial community and increases the yields of annotations by up to five folds. The metaBP toolkit demonstrates its novelty in adopting the protein-level assembly to discover small proteins, integrating protein-clustering tool in a new and flexible environment of RBiotools, and presenting the first-time small protein landscape by metaBP-ML. Taken together, metaBP (and metaBP-ML) can profile functional bacterial peptides from metagenomic samples with potential diverse mutations, in order to depict a unique landscape of small proteins from a microbial community.
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http://dx.doi.org/10.3389/fgene.2022.935351 | DOI Listing |
Cell Mol Biol (Noisy-le-grand)
January 2025
Laboratory of Plant Improvement and Valorization of Agro-resources, National School of Engineers of Sfax, University of Sfax, Sfax LR.16ES20, Tunisia.
Urinary tract infections (UTIs) are recognized as the second most common medical condition, following respiratory infections. Despite the availability of numerous efficacious antibiotics for the management of UTIs, the rising incidence of bacterial resistance presents significant challenges in the treatment of these infections. Bacteria are endowed with the ability to reproduce and develop resistance mechanisms against antibiotics.
View Article and Find Full Text PDFCell Mol Biol (Noisy-le-grand)
January 2025
Jiangxi Key Laboratory of Oncology (2024SSY06041), Jiangxi Cancer Hospital & Institute, The Second Affiliated Hospital of Nanchang Medical College, Nanchang, Jiangxi, 330029, P.R. China.
Uropathogens, particularly bacteria, can infect any part of the urinary tract and cause bacteriuria. Our study aimed to examine the antibiotic-resistant profile, associated risk factors, and phenotypic and genotypic features of ESBL, carbapenemase, and mcr resistance genes in multidrug-resistant bacteria. Samples were inoculated on culture media, identified using standard biochemical tests, and species confirmation was performed via 16S rRNA gene amplification.
View Article and Find Full Text PDFPak J Pharm Sci
January 2025
Department of Medical Microbiology, Cerrahpasa School of Medicine, Istanbul University-Cerrahpasa, Istanbul, Turkey.
Antimicrobial peptides (AMPs) may mitigate the danger of increasing antimicrobial resistance. We aimed to determine the activities of catestatin, temporin A, nisin and cecropin A against Bacteroides fragilis ATCC 25285, Prevotella melaninogenica ATCC 25845, Cutibacterium acnes ATCC 6919, Peptostreptococcus anaerobius ATCC 27337 and Peptostreptococcus stomatis DSM 17678. strains.
View Article and Find Full Text PDFXi Bao Yu Fen Zi Mian Yi Xue Za Zhi
January 2025
Department of Microbiology and Pathogenic Biology, Air Force Military Medical University, Xi'an 710032, China. *Corresponding authors, E-mail:
Objective The prevalence of drug-resistant Mycobacterium tuberculosis (Mtb) strains is exacerbating the global burden of tuberculosis (TB), highlighting the urgent need for new treatment strategies for TB. Methods The recombinant adenovirus vaccine expressing cyclic di-adenosine monophosphate (c-di-AMP) phosphodiesterase B (CnpB) (rAd-CnpB), was administered to normal mice via mucosal immunization, either alone or in combination with drug therapy, to treat Mtb respiratory infections in mice.Enzyme-linked immunosorbent assay (ELISA) was used to detect the levels of antibodies in serum and bronchoalveolar lavage fluid (BALF).
View Article and Find Full Text PDFInt J Biol Macromol
January 2025
Department of Critical Care Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China; Department of Emergency, The First Affiliated Hospital of Chongqing Medical University, Chongqing 400016, PR China. Electronic address:
Diabetic wounds often exhibit a chronic non-healing state due to the combined effects of multiple factors, including hyperglycemia, impaired angiogenesis, immune dysfunction, bacterial infection, and excessive oxidative stress. Despite the availability of various therapeutic strategies, effectively managing the complex and prolonged healing process of diabetic infected wounds remains challenging. In this study, we combined the natural antidiabetic drug lipoic acid (LA) with the RADA16-YIGSR (RY) peptide obtained through solid-phase synthesis, utilizing reversible hydrogen bonds and coordination bonds for binding.
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